* Query atom information in swig
* Atom query swig wrapping working
* SWIG wrapper for queries
* Add match to QueryAtom and QueryBond
* CShart test
* Added Java test
* Replace var with type for Java test
* Apply suggestions from code review
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Update Code/JavaWrappers/Queries.i
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Apply suggestions from code review
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Get SWIG build working again
* Remove trailing whitespace from Queries.i
* Update Queries.i to use shared_ptr
* small simplification
* remove boost::make_iterator from ROMol.i
* further simplification
---------
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* support generalized substructure search in the SubstructLibrary
* simplify namespaces
* support the new functionality in the swig wrappers
* update mac swig version in CI
* ensure swig4
* switch mac_java ci builds to conda-forge
* change in response to review
* add copy ctor to extendedquerymol
* Back to the way it was
* expose RDLog to SWIG wrappers
* - added a SetTee() overload that takes a filename as parameter to simplify redirecting from wrappers that do not have interface with C++ streams (e.g., Java and C#)
- replaced some duplicate code with ClearTee() calls
- replaced RDLogger std::shared_ptr with boost::shared_ptr to make it more easily available from SWIG wrappers
- exposed the RDLogger methods to SWIG wrappers
- added Java test for RDLogger
* this should fix the segfault
* avoid issues on case-insensitive platforms
* here's a solution keeping std:;shared_ptr
* change in response to review
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* support read-only access to cstates from python
* expose GetBrackets
* expose getAttachPoints too
remove vestigial SubstanceGroupCState_VECT
* backup
* backup
* basics working
* backup
* add label_mol_abbreviations
* fix a bug in the chirality handling
* add linkers, needs more testing
* add another peptide test
* sanitize results by default
* just need rings
* getting started with the C++ form of abbreviations
* a bit of error handling
* add findApplicableMatches
* actually apply the abbreviations
* make the getDefault functions more efficient
* add labeling (creating s groups)
* docs
* basic python wrappers (maybe this is enough?)
* add _displayLabel and _displayLabelW support to MolDraw2D
update the docs for that
* use displayLabel props
* add more default abbrevs
* change default linker defns
add parseLinkers convenience function
* make sure attachment point atoms aren't aromatic
* change the color of dummies to be darker gray
* remove python implementation
* support abbreviations in the java wrappers
* add abbreviations to the csharp wrappers
* add abbreviations to the js wrappers
* add molParity to the list of atom props not written to CXSMILES
* support condensing SUP substance groups
* add that to the python wrappers
* Update testAbbreviations.py
* clear ring info if we added it
* document that the molecules with abbreviations removed have not been sanitized
* backup
* compiles
* progress, but not there yet
* basics now working
* start towards adding another test
* test having two variation points
* add actual enumeration and the corresponding tests
* docs and cleanup
* cleanups to get the mac build working
* attempt to get win32 dll builds to work
* dlls are fun
* Add FixedMolSizeMolBundle class
* changes in response to review
Also: add warnings for bad input in ParseV3000Array
* a bit of refactoring
* additional testing
* does not work, backup
* LINKNODES work now
* cleanup
* allow silencing reaction validation warnings during initialization
* docs
* fix (and test) handling of empty enumerations
* silence warnings when doing alchemy
* first pass at a Python wrapper for the enumerator
* Add Java wrappers for MolBundle and the MolEnumerator
* cleanup some comment formatting
* TautomerQuery class
* working test
* Comment header
* Merge with master. Greg's suggestions. More tests. Python wrapper
* Updated Pattern Fingerprints to merge with master. Reset email
* Java/C# wrappers. Java test
* Java/C# wrappers. Java test
* Java/C# wrappers. Java test
* Greg suggestions of 6_2_2020
* Explicit types in Java TautomerQueryTests class
* Update Code/GraphMol/QueryOps.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* get windows dll builds working
* Removed tautomer query wrappers from RDKit namespace
* Fixes from evaluation
* Template molecule identification fix. Greg's suggestion
* Final check search functor for evaluating template matches as they are found
Co-authored-by: Gareth Jones <gjones@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* backup
* backup
* backup
* getting close to v0.1
* switch to using node indices
* add pruning and flattening
* support multiple mols
* example notebook
* backup
* initial commit
Just includes the basic API and flatten
* add the pruning step
* add removeAttachmentPoints()
* add makeScaffoldGeneric()
* improve compilation speed by adding catch_main.cpp
* add getMolFragments()
* doc cleanup
* actually add the network building code
* first pass at python wrapper
* allow edges to be nicely converted to strings
* get node counts working
* backup python notebook
* switch example notebook to use wrapped C++ code
* add BRICS fragmentation option
* fix a bug with removing attachment points to aromatic heteroatoms
* add provisional attachment point merger to notebook
* fix a bug with includeScaffoldsWithAttachments=false
* backup of efforts to get this working on windows
* backup of efforts to get this working on windows
* does not work. backup
* Fix a substructure crash on Windows
* re-enable tests
* adjust to the new BRICS form
* in-code documentation
* more doc updates
* reformat
* change the string output format for edges
* remove old python implementation
* remove obsolete test
* include a generic scaffold for the pruned structure too
* default to keepOnlyFirstFragment=false with BRICS params
* bug in removal of attachment points from generic scaffolds
* more testing
* support working from std::shared_ptr as well as boost::shared_ptr
* more testing
* disable debug printing
* use memo-ization in getMolFragments() to avoid duplicate work
* add SWIG wrapper and basic testing
* add define for RDK_USE_BOOST_SERIALIZATION
* add serialization at the C++ level
* add a string ctor for a scaffold networks
* add pickle support on the python side
* formatting
* remove old notebook
* move the fantastically useful iterable_convertor to RDBoost/Wrap.h
* expose parameter constructor with std::vector<std::string>
* add scaffoldnetwork to documentation
* add AtomValenceException
* refactor a bit and add KekulizeException
* add copy ctor and copy() method
* add detectChemistryProblems
* add getType() method
want to be able to get the type of the exception without requiring doing a bunch of dynamic casts
* first pass at exception inheritance/translation
needs some cleanup and expansion, but this does pass all tests.
* cleanup and finish the python wrappers for the new exceptions
* make sure things are truly polymorphic
* wrap shared_ptrs of the new exception types
* expose DetectChemistryProblems()
* get the java wrappers building again
* transfer those changes to the c# wrapper
* add detectChemistryProblems()
and deal with the fun fun exception inheritance things that ensue
* response to review
* Move RDBoostStreams to RDStreams
* RDBoostStreams->RDStreams
* RDBoostStreams->RDStreams
* Wrap SWIG (with Java test)
* Fix missing declaration
* Use the file that already exists
* Revert to original version
* Revert to CXSMiles version
* Update boost version
* Remove redundant code
* Add zlib
* check for win32
* FileParsers now builds static on windows
* change to make the SWig builds work on windows
* add the wrapper. Still needs tests
* first rgd java wrapper test, does not pass
* get static builds working on windows
* short test file for MolVS standardize_sm
* short test file for MolVS fragment
* short test file for MolVS metals
* short test file for MolVS normalize
* short test file for MolVS reionize
* short test file for MolVS tautomer
* short test file for MolVS validate
* long test file for MolVS standardize smiles
* long test file for MolVS fragment
* long test file for MolVS metals
* long test file for MolVS normalize
* long test file for MolVS reionize
* long test file for MolVS tautomer
* long test file for MolVS validate
* Unit tests for MolVS steps
* dropping support for Python2
* molvs/__init__.py
* molvs/charge.py
* molvs/errors.py
* molvs/fragment.py
* molvs/metal.py
* molvs/normalize.py
* molvs/resonance.py
* molvs/standardize.py
* molvs/tautomer.py
* molvs/utils.py
* molvs/validate.py
* molvs/validations.py
* molvs/cli.py
* adapted and renamed molvs/cli.py to work within $RDBASE/Contrib/MolVS/
* setup MolStandardize directories, source with empty cleanup function, header, CMake files
* corrections to empty source, header and test1.cpp
* adding empty functions and initializers to MolStandardize
* empty Metal source, header and added test
* added most of Metal.cpp functionality and made some more tests
* empty functions and initializers to Normalize
* empty functions and initializers to Validate
* added most code for RDKitDefault mode, along with some tests
* restructure for abstract base class ValidateMethod
* written in isNoneValidation for MolVSValidation
* took out isNoneValidation, put in noAtomValidation, neutralValidation, isotopeValidation for MolVSValidation
* added in AllowedAtoms
* added in disallowedAtoms
* corrections to Validate
* added code for FragmentRemover
* extended fragment functionality to include choose largest fragment, added in tests for fragment catalog, fragment remover. Also added fragmentValidation method in MolStandardize
* added another test to testValidate test_fragment
* corrections to fragment
* corrections to Metal
* added code for Normalize
* added normalize member function to MolStandardize and added tests
* added multi fragment functionality to Normalize.cpp and additional tests
* TransformCatalog
* tests for Normalize.cpp
* first bit of cleanup
* added most of Charge functionality and some tests
* some corrections to Charge.cpp and some more tests to testCharge.cpp
* corrections to Charge.cpp
* start of Tautomer Enumerate with some tests
* added BondType option to Tautomer Enumeration
* correcting for some memory leakage
* a few alterations to formatting
* sorting out some memory leaks
* sorting out some memory leaks
* some corrections for PCS test set
* redo tests with updated RDKit
* fixing memory leak
* more fixes after 100kPCS set testing
* using tab as delimiter in CSVs rather than comma
* tutorial for MolStandardize
* still working on Tautomer enumeration
* deleted some empty tests
* starting writing tautomer canonicalize
* rename test_data -> data (the source still needs to be updated)
* automatic source reformatting
* adjust to directory rename
* move the fragment catalog test into the MolStandardize directory
do not create separate library for FragmentCatalog
* stop building separate libraries for the catalogs
* move the CleanupParameters into the MolStandardize namespace
* first pass at python wrapper
* move the py module to the correct dir;
add some python tests;
add standardizeSmiles to python wrapper
* disabling the compareMolVSTest since that requires command line arguments to run
* get this building on windows
* put the python lib in the right place
* further work on python wrapper for rdMolStandardize
* added get and set functions to Metal and wrapped them
* added get and set functions to Metal and wrapped them
* changed construstor of Reionizer class and input args for reionize, wrapped this default
* overload Reionizer constructor so user can input own AcidBaseFile from python
* added Uncharger class to Charge and added test for Uncharger
* wrapped Fragment, fixed some memory leakage, changed some args and return types, added some tests
* wrapped Normalized and changed how Normalizer class is initiated
* changing MolVSValidation structure so user can choose which MolVS submethod they want
* starting to write Wrap for Validate
* now it compiles with Wrap/Validate.cpp
* a couple refactorings around validate
* move the validate code into the rdMolStandardize module
* make sure a valid pointer is returned for standardizeSmiles
* rdMolStandardize.MolVSValidation done and tests added
* half way through AllowedAtomsValidation
* finished AllowedAtomsValidation and DisallowedAtomsValidation
* moved charge, fragment, metal, normalize into the rdMolStandardize module
* changed tutorial to use wrapped code
* added copyrights
* added copyrights
* move the data files
* modify source files to adjust to the move
* added validateSmiles functionality
* removed std::cout
* redid some of the 100k PCS tests
* working on the tutorial
* adding some documentation
* deleting some comment lines
* some changes after pull review
* More changes after pull review
* start of trying to make java wrap
* remove some warnings, add some questions
* additional warning removals, a bit more reporting
* some test cleanups
* enable testing of the java code
* add a couple test files
* backup
* first pass at some theory documentatin
* it's a draft
* Update enhanced stereochemistry documentation
Adds initial target use case and caveats about the tentative
nature of the current implementation.
* Support read/write of molfile enhanced stereochemistry
This includes reading and writing of enhanced stereochemistry
from v3000 molfiles (sdf). Enhanced stereochemistry encodes
the relative configuration of stereocenters, allowing
representation of racemic mixtures and compounds with
unknown absolute stereochemistry.
It does not include:
* Python wrapping
* invalidation of the enhanced stereochemistry
* use of enhanced stereochemistry in search
* depiction of enhanced stereochemistry.
* Update to reflect changes from #1971
* change names of enum elements to allow compilation in VS2017
I think it's also clearer to do things this way
* Addressed most review comments.
* Run missed test "testEnhancedStereoChemistry"
* In tests, added size checks to group equality checks
* Updated copyright statements
* Deleted mol created for a test
* Use perfect forwarding in RWMol::setStereoGroups()
* use references for stereo groups that are checked in write and pickle
* Updated stereogroup.h in hopes of fixing compilation on Windows.
* clang-format
* try allowing a switch to boost regex and requiring it for g++-4.8
* do a better job of that
* typo
* Code review comments. Updated Copyright notice.
* When an atom is deleted, delete stereo groups containing it.
Also updates StereoGroup toUse accessors instead of
constant member attributes. This allows move of StereoGroups.
* RDKit style guide
* Add header required on Windows.
* get the SWIG wrappers to build
* this is a rough first pass, needs to be finished and is a strong argument for changing the names of some of the #defines that are currently used
* rationalize the rest of the #defines
add something to the release notes about this
* Fixes csharp build for 64 bit systems
* Need to support make and make install stages
* switch to an alternate strategy and get it working for the java wrappers too
this now builds for me on 64bit win10 with MSVC14
* add missing files from that last commit
* Hopefully fixes unix and osx builds while maintaining msvc builds
* Fixes mono builds, removes python check
* Adds RDAny (smaller generic holder) Updates all used dictionaries
This is an API compliant version of the current rdany system,
but uses a lot less memory in practice.
* Removes code duplication
* Converts CHECK_INVARIANT to TEST_ASSERT
* Fixes DoubleTag issue
* Adds Bool to DoubleMagic implementation
* Removes reference to property pickler
